Donald Trump has fired James Comey as FBI director in a move that has raised concerns over the independence of the bureau’s investigation into links between the Trump campaign and Russia in the run-up to last year’s US presidential election.

The president cited Comey’s handling of the Hillary Clinton email investigation as the reason behind his decision, but Democrats were quick to cry foul, and there were vociferous demands for a special prosecutor to be appointed to oversee the Russia inquiry. One Senate Democrat described the move as “Nixonian”.

On Tuesday, CNN reported that a grand jury had begun issuing subpoenas to associates of Michael Flynn, the former national security adviser at the centre of the ongoing inquiry into Russian meddling in the election. If confirmed, the report suggests that the FBI’s investigation into the Trump camp’s links with Moscow has entered a significant new phase.

In a letter to Comey, the president wrote: “While I greatly appreciate you informing me, on three separate occasions, that I am not under investigation, I nevertheless concur with the judgment of the Department of Justice that you are not able to effectively lead the bureau.

“It is essential that we find new leadership for the FBI that restores public trust and confidence in its vital law enforcement mission.”

Comey incorrectly testified that former Clinton aide Huma Abedin “forwarded hundreds and thousands” of emails to her husband’s laptop, including some with classified information. On Tuesday, the FBI informed the Senate judiciary committee that only “a small number” of the thousands of emails found on the laptop had been forwarded there, while most had simply been backed up from electronic devices.

Comey had also been fiercely criticised for holding a press conference last July in which he said Clinton would not be charged but criticised her as “extremely careless”. The move was seen as infringing on the role of the justice department and attorney general.

The timing of Comey’s dismissal was related to the recent confirmation of Rod Rosenstein as deputy attorney general, according to the White House. In a memo released on Tuesday, Rosenstein wrote: “The director was wrong to usurp the attorney general’s authority on 5 July 2016, and announce his conclusion that the [Clinton] case should be closed without prosecution.”

The memo added: “Compounding the error, the director ignored another longstanding principle: we do not hold press conferences to release derogatory information about the subject of a declined criminal investigation … the director laid out his version of the facts for the news media as if it were a closing argument, but without a trial.

“It is a textbook example of what federal prosecutors and agents are taught not to do.”

A statement from the White House said: “Today, President Donald J Trump informed FBI director James Comey that he has been terminated and removed from office. President Trump acted based on the clear recommendations of both Deputy Attorney General Rod Rosenstein and Attorney General Jeff Sessions.”

The search for the next head of “our crown jewel of law enforcement” will begin immediately, the statement said. Comey’s deputy, Andrew McCabe, takes over in the interim.

Former FBI director James Comey testifies on Capitol Hill in Washington before a Senate judiciary committee hearing.Photograph: Carolyn Kaster/AP

Comey, 56, who was nominated by Barack Obama in 2013 to a 10-year term, reportedly found out he had been fired from breaking news alerts on TV screens as he delivered a speech to FBI staff in Los Angeles. He was “caught flat-footed” but carried on talking to the agents, the Los Angeles Times reported.

Soon after, in another bizarre turn, a letter was hand delivered to FBI headquarters in Washington by Keith Schiller, Trump’s former bodyguard who worked for Trump’s security team for nearly two decades before joining the administration.

The last US president to fire an FBI director was Bill Clinton, who dismissed William Sessions in 1993 over financial irregularities.

Comey’s dismissal raises questions over the future of the FBI’s investigation into alleged ties between Trump associates and Russia during the presidential election.

While the Republican majorities in the House and Senate could hold back congressional investigations and a new FBI director to kill off its counter-intelligence investigation, a grand jury is not under Trump’s control. He may not be able to stop the Russian collusion affair from going to court.

Under US law, grand juries (which are larger than normal 12-person court juries) have sweeping powers to compel witnesses to appear, to call for the presentation of documents and to issue indictments.

Most Republicans backed the president, including the Senate judiciary committee chairman, Chuck Grassley, who said: “The handling of the Clinton email investigation is a clear example of how Comey’s decisions have called into question the trust and political independence of the FBI …The effectiveness of the FBI depends upon the public trust and confidence. Unfortunately, this has clearly been lost.”

But broad condemnation from Democrats and dissent from some Republicans is likely to intensify pressure for the appointment of a special prosecutor.

Justin Amash, a Republican congressman from Michigan, tweeted: “My staff and I are reviewing legislation to establish an independent commission on Russia.” He described the justification given in Trump’s letter to Comey as “bizarre”.

Democrat Adam Schiff, ranking member of the House intelligence committee, said: “The same president who has called the investigation into the Russian hacking of our democracy and the potential complicity of his campaign a ‘fake’ cannot pretend to have made such a decision uninfluenced by his concerns over Comey’s continued involvement in the investigation.

“It is more imperative than ever that an independent prosecutor be appointed.”

Senator Bob Casey, a Democrat from Pennsylvania, said: “This is Nixonian. Deputy Attorney General Rod Rosenstein must immediately appoint a special counsel to continue the Trump/Russia investigation … this investigation must be independent and thorough in order to uphold our nation’s system of justice.”

Chuck Schumer, Democratic minority leader in the Senate, said he told Trump, who called to notify him before making the firing public, “you’re making a very big mistake.”

He added: “If deputy attorney general Rosenstein does not appoint an independent special prosecutor, every American will rightly suspect that the decision to fire director Comey was part of a cover-up.”

Schumer has taken the unusual move of asking all Democratic Senators to be in their seats at 9.30am on Wednesday, NBC Nightly News reported.

Trump accused Schumer of hypocrisy. He fired back on Twitter: “Cryin’ Chuck Schumer stated recently, “I do not have confidence in him (James Comey) any longer.” Then acts so indignant. #draintheswamp”

Civil society groups also expressed alarm at the day’s events. Anthony Romero, executive director of the American Civil Liberties Union, said: “The independence of the FBI director is meant to ensure that the president does not operate above the law. For President Trump to fire the man responsible for investigating his own campaign’s ties to the Russians imperils that fundamental principle.”

The president only has one publicly scheduled item on his agenda on Wednesday: a meeting with Sergey Lavrov, the foreign minister of Russia.

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